Commit e591e5df authored by Pradat Yoann's avatar Pradat Yoann

update README with install details

parent 6e22150e
......@@ -25,7 +25,7 @@ vcf2maf also runs VEP internally but performs extra work to build some annotatio
- *Reference_Allele*
- *Tumor_Seq_Allele1* (can be discarded)
- *Tumor_Seq_Allele2* (can be discarded)
- *dnSNP_RS*
- *dbSNP_RS*
- *HGVS_p*
- *HGVS_c*
- *HGVS_Short*
......@@ -38,3 +38,40 @@ that are not available from VEP's output.
Run the VEP annotator on the VCF file from a specific set of options. The options can be changed in the code if required.
## 2. How to run the tool ?
### 2.1 Install VEP
Clone VEP from the [official github](https://github.com/Ensembl/ensembl-vep). Installation details are provided there. As specified, run
```
git clone https://github.com/Ensembl/ensembl-vep
cd ensembl-vep
perl INSTALL.pl
```
The perl script INSTALL.pl may return errors as missing dependencies or other. For instance,the error `Bio::Root::Version is not installed` may be solved by running `sudo cpanm Bio::Root::Version`. You may have more than one such library to install. Refer to the github for the details.
The installation from the perl script offers the choice to install cache files (most efficient use of vep) and FASTA files (to retrieve sequence data for HGVS notations) into `$HOME/.vep`. You may also install plugins for additional analyses. Download cache files for Homo Sapiens genome 99_GRCh37 (or newer). The total download size is about 12 GB of data so a stable and fast connection is required here. The FASTA file Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz requires 882 MB of storage. *DO NOT FORGET* to unzip this file (or VEP will fail).
### 2.2 Install vcf2maf
VEP is required by vcf2maf may you need also need the set of commands `samtools`, and `htslib` available at [http://www.htslib.org/download/](http://www.htslib.org/download/). Do the following
```
cd samtools-1.x
./configure --prefix=/where/to/install
make
make install
ln -s /where/to/install/bin/samtools /usr/local/bin
cd htslib −1.x
./configure −−prefix=/where/to/install
make
make install
ln −s /where/to/install/bin/htslib /usr/local/bin
ln −s /where/to/install/bin/tabix /usr/local/bin
ln −s /where/to/install/bin/bgzip /usr/local/bin
```
You may replace `/usr/local/bin` with whatever path where you usually save binaries. Finish the installation of vcf2maf following the instructions given in the [github](https://github.com/mskcc/vcf2maf).
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